To acquire or resist: The complex biological effects of CRISPR-Cas systems

Trends in Microbiology

Volumn 22, Issue 4, 2014, Pages 218-225

  Bondy Denomy, Joseph ^a   Davidson, Alan R ^a  

^a UNIVERSITY OF TORONTO   (Canada)

Author keywords

Anti CRISPR; CRISPR Cas; Horizontal gene transfer; Mobile DNA; Phage resistance; Prophage

Indexed keywords

BACTERIAL GENOME; COST BENEFIT ANALYSIS; CRISPR CAS SYSTEM; GENE INTERACTION; GENE LOCUS; GENETIC VARIABILITY; GENOME ANALYSIS; NONHUMAN; PREVALENCE; PRIORITY JOURNAL; PROKARYOTE; REVIEW; RNA SEQUENCE;

BACTERIA (MICROORGANISMS); PROKARYOTA;

ANTI-CRISPR; CRISPR-CAS; HORIZONTAL GENE TRANSFER; MOBILE DNA; PHAGE RESISTANCE; PROPHAGE;

ADAPTATION, BIOLOGICAL; CRISPR-CAS SYSTEMS; EVOLUTION, MOLECULAR; PROKARYOTIC CELLS; RECOMBINATION, GENETIC;

EID: 84897440729     PISSN: 0966842X     EISSN: 18784380     Source Type: Journal    
DOI: 10.1016/j.tim.2014.01.007     Document Type: Review

References (82)

1. Ishino Y., et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J. Bacteriol. 1987, 169:5429-5433.
2. Jansen R., et al. Identification of genes that are associated with DNA repeats in prokaryotes. Mol. Microbiol. 2002, 43:1565-1575.
3. Mojica F.J.M., et al. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 2005, 60:174-182.
4. Pourcel C., et al. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 2005, 151:653-663.
5. Bolotin A., et al. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology 2005, 151:2551-2561.
6. Barrangou R., et al. CRISPR provides acquired resistance against viruses in prokaryotes. Science 2007, 315:1709-1712.
7. Grissa I., et al. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007, 35:W52-W57.
8. Makarova K.S., et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 2011, 9:467-477.
9. Bhaya D., et al. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu. Rev. Genet. 2011, 45:273-297.
10. Deltcheva E., et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 2011, 471:602-607.
11. Haurwitz R.E., et al. Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science 2010, 329:1355-1358.
12. Sternberg S.H., et al. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA 2012, 18:661-672.
13. Brouns S.J.J., et al. Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 2008, 321:960-964.
14. Garneau J.E., et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2010, 468:67-71.
15. Marraffini L.A., Sontheimer E.J. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 2008, 322:1843-1845.
16. Hale C.R., et al. RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex. Cell 2009, 139:945-956.
17. Mojica F.J.M., et al. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009, 155:733-740.
18. Labrie S.J., et al. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 2010, 8:317-327.
19. Samson J.E., et al. Revenge of the phages: defeating bacterial defences. Nat. Rev. Microbiol. 2013, 11:675-687.
20. Stern A., et al. CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome. Genome Res. 2012, 22:1985-1994.
21. Rho M., et al. Diverse CRISPRs evolving in human microbiomes. PLoS Genet. 2012, 8:e1002441.
22. Reeks J., et al. CRISPR interference: a structural perspective. Biochem. J. 2013, 453:155-166.
23. Westra E.R., et al. The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity. Annu. Rev. Genet. 2012, 46:311-339.
24. Levin B.R. Nasty viruses, costly plasmids, population dynamics, and the conditions for establishing and maintaining CRISPR-mediated adaptive immunity in bacteria. PLoS Genet. 2010, 6:e1001171.
25. Navarre W.W., et al. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 2006, 313:236-238.
26. Weinberger A.D., Gilmore M.S. CRISPR-Cas: to take up DNA or not-that is the question. Cell Host Microbe 2012, 12:125-126.
27. Cady K.C., et al. The CRISPR/Cas adaptive immune system of Pseudomonas aeruginosa mediates resistance to naturally occurring and engineered phages. J. Bacteriol. 2012, 194:5728-5738.
28. Edgar R., Qimron U. The Escherichia coli CRISPR system protects from lysogenization, lysogens, and prophage induction. J. Bacteriol. 2010, 192:6291-6294.
29. Vercoe R.B., et al. Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet. 2013, 9:e1003454.
30. Yosef I., et al. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 2012, 40:5569-5576.
31. Manica A., et al. In vivo activity of CRISPR-mediated virus defence in a hyperthermophilic archaeon. Mol. Microbiol. 2011, 80:481-491.
32. Stern A., et al. Self-targeting by CRISPR: gene regulation or autoimmunity?. Trends Genet. 2010, 26:335-340.
33. Nozawa T., et al. CRISPR inhibition of prophage acquisition in Streptococcus pyogenes. PLoS ONE 2011, 6:e19543.
34. Palmer K.L., Gilmore M.S. Multidrug-resistant enterococci lack CRISPR-Cas. MBio 2010, 1:e00227-e310.
35. Dugar G., et al. High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet. 2013, 9:e1003495.
36. Jiang W., et al. Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genet. 2013, 9:e1003844.
37. Deveau H., et al. Phage response to CRISPR-encoded resistance in Streptococcus thermophilus. J. Bacteriol. 2008, 190:1390-1400.
38. Avery O.T., et al. Studies on the chemical nature of the substance inducing transformation of pneuomococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus Type III. J. Exp. Med. 1944, 79:137-158.
39. Bikard D., et al. CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection. Cell Host Microbe 2012, 12:177-186.
40. Jorth P., Whiteley M. An evolutionary link between natural transformation and CRISPR adaptive immunity. MBio 2012, 3:e00309-e312.
41. Zhang Y., et al. Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol. Cell 2013, 50:488-503.
42. Godde J.S., Bickerton A. The repetitive DNA elements called CRISPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J. Mol. Evol. 2006, 62:718-729.
43. Scholz I., et al. CRISPR-Cas systems in the cyanobacterium Synechocystis sp. PCC6803 exhibit distinct processing pathways involving at least two Cas6 and a Cmr2 protein. PLoS ONE 2013, 8:e56470.
44. Yang Y., et al. pSLA2-M of Streptomyces rochei is a composite linear plasmid characterized by self-defense genes and homology with pSLA2-L. Biosci. Biotechnol. Biochem. 2011, 75:1147-1153.
45. Millen A.M., et al. Mobile CRISPR/Cas-mediated bacteriophage resistance in Lactococcus lactis. PLoS ONE 2012, 7:e51663.
46. Sebaihia M., et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat. Genet. 2006, 38:779-786.
47. Soutourina O.A., et al. Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile. PLoS Genet. 2013, 9:e1003493.
48. Minot S., et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 2011, 21:1616-1625.
49. Minot S., et al. Rapid evolution of the human gut virome. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:12450-12455.
50. Seed K.D., et al. A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 2013, 494:489-491.
51. Pul U., et al. Identification and characterization of E. coli CRISPR-Cas promoters and their silencing by H-NS. Mol. Microbiol. 2010, 75:1495-1512.
52. Touchon M., et al. CRISPR distribution within the Escherichia coli species is not suggestive of immunity-associated diversifying selection. J. Bacteriol. 2011, 193:2460-2467.
53. Touchon M., Rocha E.P.C. The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS ONE 2010, 5:e11126.
54. Touchon M., et al. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology 2012, 158:2997-3004.
55. Westra E.R., et al. H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO. Mol. Microbiol. 2010, 77:1380-1393.
56. Medina-Aparicio L., et al. The CRISPR/Cas immune system is an operon regulated by LeuO, H-NS, and leucine-responsive regulatory protein in Salmonella enterica serovar Typhi. J. Bacteriol. 2011, 193:2396-2407.
57. Bondy-Denomy J., et al. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 2013, 493:429-432.
58. Makarova K.S., et al. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol. Direct 2006, 1:7.
59. Schunder E., et al. First indication for a functional CRISPR/Cas system in Francisella tularensis. Int. J. Med. Microbiol. 2013, 303:51-60.
60. Sampson T.R., et al. A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 2013, 497:254-257.
61. Mandin P., et al. Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res. 2007, 35:962-974.
62. Zegans M.E., et al. Interaction between bacteriophage DMS3 and host CRISPR region inhibits group behaviors of Pseudomonas aeruginosa. J. Bacteriol. 2009, 191:210-219.
63. Cady K.C., O'toole G.A. Non-identity-mediated CRISPR-bacteriophage interaction mediated via the Csy and Cas3 proteins. J. Bacteriol. 2011, 193:3433-3445.
64. Semenova E., et al. Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:10098-10103.
65. Biswas A., et al. CRISPRTarget: bioinformatic prediction and analysis of crRNA targets. RNA Biol. 2013, 10:817-827.
66. Babu M., et al. A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol. Microbiol. 2011, 79:484-502.
67. Gunderson F.F., Cianciotto N.P. The CRISPR-associated gene cas2 of Legionella pneumophila is required for intracellular infection of amoebae. MBio 2013, 4. e00074-13. doi:10.1128/mBio.00074-13.
68. Lopez-Sanchez M-J., et al. The highly dynamic CRISPR1 system of Streptococcus agalactiae controls the diversity of its mobilome. Mol. Microbiol. 2012, 85:1057-1071.
69. Gudbergsdottir S., et al. Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers. Mol. Microbiol. 2011, 79:35-49.
70. Erdmann S., Garrett R.A. Selective and hyperactive uptake of foreign DNA by adaptive immune systems of an archaeon via two distinct mechanisms. Mol. Microbiol. 2012, 85:1044-1056.
71. Fischer S., et al. An archaeal immune system can detect multiple protospacer adjacent motifs (PAMs) to target invader DNA. J. Biol. Chem. 2012, 287:33351-33363.
72. Elmore J.R., et al. Programmable plasmid interference by the CRISPR-Cas system in Thermococcus kodakarensis. RNA Biol. 2013, 10:828-840.
73. Almendros C., et al. Target motifs affecting natural immunity by a constitutive CRISPR-Cas system in Escherichia coli. PLoS ONE 2012, 7:e50797.
74. Delaney N.F., et al. Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum. PLoS Genet. 2012, 8:e1002511.
75. Semenova E., et al. Analysis of CRISPR system function in plant pathogen Xanthomonas oryzae. FEMS Microbiol. Lett. 2009, 296:110-116.
76. Tyson G.W., Banfield J.F. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ. Microbiol. 2008, 10:200-207.
77. Andersson A.F., Banfield J.F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 2008, 320:1047-1050.
78. Cui Y., et al. Insight into microevolution of Yersinia pestis by clustered regularly interspaced short palindromic repeats. PLoS ONE 2008, 3:e2652.
79. Held N.L., et al. Reassortment of CRISPR repeat-spacer loci in Sulfolobus islandicus. Environ. Microbiol. 2013, 10.1111/1462-2920.12146.
80. Rezzonico F., et al. Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora. Appl. Environ. Microbiol. 2011, 77:3819-3829.
81. Watanabe T., et al. CRISPR regulation of intraspecies diversification by limiting IS transposition and intercellular recombination. Genome Biol. Evol. 2013, 5:1099-1114.
82. Cady K.C., et al. Prevalence, conservation and functional analysis of Yersinia and Escherichia CRISPR regions in clinical Pseudomonas aeruginosa isolates. Microbiology 2011, 157:430-437.